Composite multiple render layers for multiple frames?
Ok so I found out my problem. Totally my fault, as I misunderstood this passage from: https://www.blender.org/manual/render/post_process/layers.html



Scene (layer)
The Scene Layers, showing which are currently visible and will be rendered.
(render) Layer
The Scene Layers which are associated with the active Render Layer. Objects in those Scene Layers will be rendered in that Render Layer. When an object is in the Scene Layers but not the Render Layer, it will still cast shadows and be visible in reflections, so it is still indirectly visible.



I had setup two render layers, one of which contained scene layer 1, and the other scene layer 2. I tried rendering by having only one scene layer visible. Here is where the confusing part is. When 2 scene layers are visible (or more) and I run a smoke simulation, it shows that my flow objects from scene one are pouring into my smoke domain from scene 2. However, if you render properly, even though the simulation shows up that way, the render still comes out right. I just got lost in the confusion but pulled myself out eventually.